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Items: 31

1.

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.

Sharma AK, Sormanni P, Ahmed N, Ciryam P, Friedrich UA, Kramer G, O'Brien EP.

PLoS Comput Biol. 2019 May 23;15(5):e1007070. doi: 10.1371/journal.pcbi.1007070. eCollection 2019 May.

2.

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming.

Ahmed N, Sormanni P, Ciryam P, Vendruscolo M, Dobson CM, O'Brien EP.

Sci Rep. 2019 Apr 18;9(1):6256. doi: 10.1038/s41598-019-42348-x.

3.

Different soluble aggregates of Aβ42 can give rise to cellular toxicity through different mechanisms.

De S, Wirthensohn DC, Flagmeier P, Hughes C, Aprile FA, Ruggeri FS, Whiten DR, Emin D, Xia Z, Varela JA, Sormanni P, Kundel F, Knowles TPJ, Dobson CM, Bryant C, Vendruscolo M, Klenerman D.

Nat Commun. 2019 Apr 4;10(1):1541. doi: 10.1038/s41467-019-09477-3.

4.

A method of predicting the in vitro fibril formation propensity of Aβ40 mutants based on their inclusion body levels in E. coli.

Sanagavarapu K, Nüske E, Nasir I, Meisl G, Immink JN, Sormanni P, Vendruscolo M, Knowles TPJ, Malmendal A, Cabaleiro-Lago C, Linse S.

Sci Rep. 2019 Mar 6;9(1):3680. doi: 10.1038/s41598-019-39216-z.

5.

Protein Solubility Predictions Using the CamSol Method in the Study of Protein Homeostasis.

Sormanni P, Vendruscolo M.

Cold Spring Harb Perspect Biol. 2019 Mar 4. pii: a033845. doi: 10.1101/cshperspect.a033845. [Epub ahead of print]

PMID:
30833455
6.

In vitro and in silico assessment of the developability of a designed monoclonal antibody library.

Wolf Pérez AM, Sormanni P, Andersen JS, Sakhnini LI, Rodriguez-Leon I, Bjelke JR, Gajhede AJ, De Maria L, Otzen DE, Vendruscolo M, Lorenzen N.

MAbs. 2019 Feb/Mar;11(2):388-400. doi: 10.1080/19420862.2018.1556082. Epub 2019 Jan 18.

PMID:
30523762
7.

Attentive Cross-Modal Paratope Prediction.

Deac A, VeliČković P, Sormanni P.

J Comput Biol. 2019 Jun;26(6):536-545. doi: 10.1089/cmb.2018.0175. Epub 2018 Dec 1.

PMID:
30508394
8.

Third generation antibody discovery methods: in silico rational design.

Sormanni P, Aprile FA, Vendruscolo M.

Chem Soc Rev. 2018 Dec 10;47(24):9137-9157. doi: 10.1039/c8cs00523k. Review.

PMID:
30298157
9.

A Rationally Designed Hsp70 Variant Rescues the Aggregation-Associated Toxicity of Human IAPP in Cultured Pancreatic Islet β-Cells.

Bongiovanni MN, Aprile FA, Sormanni P, Vendruscolo M.

Int J Mol Sci. 2018 May 12;19(5). pii: E1443. doi: 10.3390/ijms19051443.

10.

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity.

Le Marchand T, de Rosa M, Salvi N, Sala BM, Andreas LB, Barbet-Massin E, Sormanni P, Barbiroli A, Porcari R, Sousa Mota C, de Sanctis D, Bolognesi M, Emsley L, Bellotti V, Blackledge M, Camilloni C, Pintacuda G, Ricagno S.

Nat Commun. 2018 Apr 25;9(1):1658. doi: 10.1038/s41467-018-04078-y.

11.

Parapred: antibody paratope prediction using convolutional and recurrent neural networks.

Liberis E, Velickovic P, Sormanni P, Vendruscolo M, Liò P.

Bioinformatics. 2018 Sep 1;34(17):2944-2950. doi: 10.1093/bioinformatics/bty305.

PMID:
29672675
12.

Corneal Dystrophy Mutations Drive Pathogenesis by Targeting TGFBIp Stability and Solubility in a Latent Amyloid-forming Domain.

Stenvang M, Schafer NP, Malmos KG, Pérez AW, Niembro O, Sormanni P, Basaiawmoit RV, Christiansen G, Andreasen M, Otzen DE.

J Mol Biol. 2018 Apr 13;430(8):1116-1140. doi: 10.1016/j.jmb.2018.03.001. Epub 2018 Mar 7.

PMID:
29524512
13.

Massively parallel C. elegans tracking provides multi-dimensional fingerprints for phenotypic discovery.

Perni M, Challa PK, Kirkegaard JB, Limbocker R, Koopman M, Hardenberg MC, Sormanni P, Müller T, Saar KL, Roode LWY, Habchi J, Vecchi G, Fernando N, Casford S, Nollen EAA, Vendruscolo M, Dobson CM, Knowles TPJ.

J Neurosci Methods. 2018 Aug 1;306:57-67. doi: 10.1016/j.jneumeth.2018.02.005. Epub 2018 Feb 13.

PMID:
29452179
14.

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins.

Piovesan D, Tabaro F, Paladin L, Necci M, Micetic I, Camilloni C, Davey N, Dosztányi Z, Mészáros B, Monzon AM, Parisi G, Schad E, Sormanni P, Tompa P, Vendruscolo M, Vranken WF, Tosatto SCE.

Nucleic Acids Res. 2018 Jan 4;46(D1):D471-D476. doi: 10.1093/nar/gkx1071.

15.

Delivery of Native Proteins into C. elegans Using a Transduction Protocol Based on Lipid Vesicles.

Perni M, Aprile FA, Casford S, Mannini B, Sormanni P, Dobson CM, Vendruscolo M.

Sci Rep. 2017 Nov 8;7(1):15045. doi: 10.1038/s41598-017-13755-9.

16.

Oxetane Grafts Installed Site-Selectively on Native Disulfides to Enhance Protein Stability and Activity In Vivo.

Martínez-Sáez N, Sun S, Oldrini D, Sormanni P, Boutureira O, Carboni F, Compañón I, Deery MJ, Vendruscolo M, Corzana F, Adamo R, Bernardes GJL.

Angew Chem Int Ed Engl. 2017 Nov 20;56(47):14963-14967. doi: 10.1002/anie.201708847. Epub 2017 Oct 20.

17.

Rapid and accurate in silico solubility screening of a monoclonal antibody library.

Sormanni P, Amery L, Ekizoglou S, Vendruscolo M, Popovic B.

Sci Rep. 2017 Aug 15;7(1):8200. doi: 10.1038/s41598-017-07800-w.

18.

Selective targeting of primary and secondary nucleation pathways in Aβ42 aggregation using a rational antibody scanning method.

Aprile FA, Sormanni P, Perni M, Arosio P, Linse S, Knowles TPJ, Dobson CM, Vendruscolo M.

Sci Adv. 2017 Jun 21;3(6):e1700488. doi: 10.1126/sciadv.1700488. eCollection 2017 Jun.

19.

Simultaneous quantification of protein order and disorder.

Sormanni P, Piovesan D, Heller GT, Bonomi M, Kukic P, Camilloni C, Fuxreiter M, Dosztanyi Z, Pappu RV, Babu MM, Longhi S, Tompa P, Dunker AK, Uversky VN, Tosatto SC, Vendruscolo M.

Nat Chem Biol. 2017 Mar 22;13(4):339-342. doi: 10.1038/nchembio.2331. No abstract available.

PMID:
28328918
20.

A natural product inhibits the initiation of α-synuclein aggregation and suppresses its toxicity.

Perni M, Galvagnion C, Maltsev A, Meisl G, Müller MB, Challa PK, Kirkegaard JB, Flagmeier P, Cohen SI, Cascella R, Chen SW, Limbocker R, Sormanni P, Heller GT, Aprile FA, Cremades N, Cecchi C, Chiti F, Nollen EA, Knowles TP, Vendruscolo M, Bax A, Zasloff M, Dobson CM.

Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):E1009-E1017. doi: 10.1073/pnas.1610586114. Epub 2017 Jan 17. Erratum in: Proc Natl Acad Sci U S A. 2017 Mar 21;114(12 ):E2543. Limboker, Ryan [corrected to Limbocker, Ryan].

21.

A protein homeostasis signature in healthy brains recapitulates tissue vulnerability to Alzheimer's disease.

Freer R, Sormanni P, Vecchi G, Ciryam P, Dobson CM, Vendruscolo M.

Sci Adv. 2016 Aug 10;2(8):e1600947. doi: 10.1126/sciadv.1600947. eCollection 2016 Aug.

22.

Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.

Camilloni C, Sala BM, Sormanni P, Porcari R, Corazza A, De Rosa M, Zanini S, Barbiroli A, Esposito G, Bolognesi M, Bellotti V, Vendruscolo M, Ricagno S.

Sci Rep. 2016 May 6;6:25559. doi: 10.1038/srep25559.

23.

Targeting disordered proteins with small molecules using entropy.

Heller GT, Sormanni P, Vendruscolo M.

Trends Biochem Sci. 2015 Sep;40(9):491-6. doi: 10.1016/j.tibs.2015.07.004. Epub 2015 Aug 11. Review.

PMID:
26275458
24.

Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.

Sormanni P, Aprile FA, Vendruscolo M.

Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):9902-7. doi: 10.1073/pnas.1422401112. Epub 2015 Jul 27.

25.

A Rational Design Strategy for the Selective Activity Enhancement of a Molecular Chaperone toward a Target Substrate.

Aprile FA, Sormanni P, Vendruscolo M.

Biochemistry. 2015 Aug 18;54(32):5103-12. doi: 10.1021/acs.biochem.5b00459. Epub 2015 Aug 7.

PMID:
26192230
26.

The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins.

Sormanni P, Camilloni C, Fariselli P, Vendruscolo M.

J Mol Biol. 2015 Feb 27;427(4):982-996. doi: 10.1016/j.jmb.2014.12.007. Epub 2014 Dec 20.

PMID:
25534081
27.

The CamSol method of rational design of protein mutants with enhanced solubility.

Sormanni P, Aprile FA, Vendruscolo M.

J Mol Biol. 2015 Jan 30;427(2):478-90. doi: 10.1016/j.jmb.2014.09.026. Epub 2014 Oct 14.

PMID:
25451785
28.

Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein.

Gianni S, Camilloni C, Giri R, Toto A, Bonetti D, Morrone A, Sormanni P, Brunori M, Vendruscolo M.

Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):14141-6. doi: 10.1073/pnas.1405233111. Epub 2014 Sep 16.

29.

Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale.

Capelli R, Paissoni C, Sormanni P, Tiana G.

J Chem Phys. 2014 May 21;140(19):195101. doi: 10.1063/1.4876219.

PMID:
24852563
30.

Subdomain architecture and stability of a giant repeat protein.

Tsytlonok M, Sormanni P, Rowling PJ, Vendruscolo M, Itzhaki LS.

J Phys Chem B. 2013 Oct 24;117(42):13029-37. doi: 10.1021/jp402360x. Epub 2013 Sep 20.

PMID:
24053231
31.

Fibrillogenic propensity of the GroEL apical domain: a Janus-faced minichaperone.

Chen J, Yagi H, Sormanni P, Vendruscolo M, Makabe K, Nakamura T, Goto Y, Kuwajima K.

FEBS Lett. 2012 Apr 24;586(8):1120-7. doi: 10.1016/j.febslet.2012.03.019. Epub 2012 Mar 23.

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